diff --git a/modules/system/activation/activation-script.nix b/modules/system/activation/activation-script.nix
index 5c6ca55add82..8924041ae600 100644
--- a/modules/system/activation/activation-script.nix
+++ b/modules/system/activation/activation-script.nix
@@ -133,6 +133,7 @@ let
           /nix/var/nix/chroots
       mkdir -m 1777 -p /nix/var/nix/gcroots/per-user
       mkdir -m 1777 -p /nix/var/nix/profiles/per-user
+      mkdir -m 1777 -p /nix/var/nix/gcroots/tmp
 
       ln -sf /nix/var/nix/profiles /nix/var/nix/gcroots/
       ln -sf /nix/var/nix/manifests /nix/var/nix/gcroots/
diff --git a/modules/system/boot/stage-2-init.sh b/modules/system/boot/stage-2-init.sh
index 8859e5716ffb..834ad9548ed3 100644
--- a/modules/system/boot/stage-2-init.sh
+++ b/modules/system/boot/stage-2-init.sh
@@ -130,6 +130,10 @@ mkdir -m 1777 /tmp/.ICE-unix
 rm -rf /nix/var/nix/chroots # recreated in activate-configuration.sh
 
 
+# Also get rid of temporary GC roots.
+rm -rf /nix/var/nix/gcroots/tmp /nix/var/nix/temproots
+
+
 # Use a tmpfs for /var/run to ensure that / or /var can be unmounted
 # or at least remounted read-only during shutdown.  (Upstart 0.6
 # apparently uses nscd to do some name lookups, resulting in it